Resting-state functional connectivity (FC) studies have revealed that second language (L2) reading comprehension can be predicted by intrinsic functional organization (IFO) within language network. However, these studies select some specific seed regions in language network according to priori knowledge before FC analysis, which can result in some biased results and neglect of some important unpredictable findings. Additionally, most previous studies explore L2 reading comprehension largely taking reading as a global construct without considering the multidimensional structure of reading, thus little is known about the features of IFO related to subskills of reading ability in L2 learning. Therefore, the present study combines resting-state whole-brain functional connectivity density (FCD) with the FC analysis based on seed regions to investigate the characteristics of IFO associated with specific dimensions of L2 reading. Nineteen Tibetan-Chinese bilinguals were recruited in the present study and resting-state functional magnetic resonance imaging (fMRI) data were acquired in each participant. Then, the Chinese Character Reading Efficiency Test (CCRET) and the reading comprehension section of Hanyu Shuiping Kaoshi (HSK) were used to evaluate the global level and two dimensions (literal comprehension and inferential comprehension) of L2 reading respectively. Next, a novel voxel-level whole-brain FCD analysis was applied to find the key brain regions associated with L2 reading. Furthermore, the FC between key brain regions and each voxel was computed by conducting seed-based FC analysis, and the correlation between each FC and two dimensions of Chinese reading conprehension was also evaluated respectively. The results showed that literal comprehension scores in L2 reading were not only significantly correlated with inferential comprehension scores but also higher than inferential comprehension scores. FCD analysis found that the three key brain regions including the left inferior frontal gyrus, right lingual gyrus and right precuneus had significant correlations with CCRET scores. Further seed-based FC analysis revealed that both literal comprehension scores and inferential comprehension scores were positively correlated with the FC between the left inferior frontal gyrus and left superior temporal gyrus as well as between the right lingual gyrus and right precentral gyrus. Moreover, inferential comprehension scores also showed positive correlations with the FC between the left inferior frontal gyrus and right parietal lobule. These findings indicate that different dimensions of L2 reading comprehension of Tibetan-Chinese bilinguals in L2 learning have significant correlations with FC in resting state, and some specific FC circuits are involved in the processing of inferential comprehension compared with the processing of literal comprehension in L2 reading. More generally, this study also suggests that different dimensions of L2 reading comprehension can be reflected by intrinsic functional organization, thus may provide important theoretical implications in our understanding of neural processing mechanisms for L2 reading. This study differentiates itself from previous research in that it chooses seed regions of FC analysis based on a data-driven approach by conducting correlation analysis between FCD and CCRET. In addition, the present study takes reading as a multidimensional structure rather than a global construct, investigating the characteristics of intrinsic brain functional organization related to different dimensions of reading comprehension (literal comprehension and inferential comprehension) in L2 learning.